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    <title>Mapping</title>
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    <h1>
      <strong>Mapping : pSEVA uses bwa, bowtie, SOAP2 and MAQ for Mapping. </strong>
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    <p>
      <strong> bwa </strong>
    </p>
      <p>
		Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. Please see the BWA manual page for more information.
      </p>
      <p>
		Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-60. [PMID: 19451168]
	<br>
      </p>
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      <form method="post" enctype="multipart/form-data" action="bwa.jsp">
      <p>
        <strong> Align Options</strong>
      </p>
      <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Input File Name &nbsp;&nbsp;&nbsp;<input type="file" size="80" name="InputFile"/>      
      </p>
      
      <p>
         &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reference Genome 
        <select name="Reference">
          <option value="hg19">hg19</option>
          <option value="hg18">hg18</option>
        </select>
      </p>      
      
      <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Maximum edit distance(n) &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="aln_n" value="0.04"/>
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Maximum number of gap opens(o) &nbsp;&nbsp;<input type="text" size="10" name="aln_o" value="1"/>
      </p>
      <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Maximum number of gap extensions(e) &nbsp;&nbsp; <input type="text" size="10" name="aln_e" value="-1"/>
      </p>
       <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Disallow a long deletion(d) &nbsp;&nbsp; <input type="text" size="10" name="aln_d" value="16"/>
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Disallow an indel(i) &nbsp;&nbsp; <input type="text" size="10" name="aln_i" value="5"/>
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Seed length(l) &nbsp;&nbsp; <input type="text" size="10" name="aln_l" />
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Maximum edit distance(k) &nbsp;&nbsp; <input type="text" size="10" name="aln_k" value="2"/>
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Number of threads(t) &nbsp;&nbsp; <input type="text" size="10" name="aln_t" value="1"/>
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Mismatch penalty(M) &nbsp;&nbsp; <input type="text" size="10" name="aln_M" value="3"/>
      </p>
       <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Gap open penalty(O) &nbsp;&nbsp; <input type="text" size="10" name="aln_O" value="11"/>
      </p>
       <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Gap extension penalty(E) &nbsp;&nbsp; <input type="text" size="10" name="aln_E" value="4"/>
      </p>
       <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Suboptimal alignment threshold(R) &nbsp;&nbsp; <input type="text" size="10" name="aln_R" />
      </p>
       <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Color space(c) &nbsp;&nbsp; <input type="text" size="10" name="aln_c" />
      </p>
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Disable iterative search(N) &nbsp;&nbsp; <input type="text" size="10" name="aln_N" />
      </p>
       <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Read trimming parameter(q) &nbsp;&nbsp; <input type="text" size="10" name="aln_q" value="0"/>
      </p>
		<input type="submit" value="submit">
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